🧰 Tools for Developers and Semantic Engineers

🪄 Working with strings that might be a URI or a CURIE

Sometimes, it’s not clear if a string is a CURIE or a URI. While the SafeCURIE syntax is intended to address this, it’s often overlooked.

☑️ CURIE and URI Checks

The first way to handle this ambiguity is to be able to check if the string is a CURIE or a URI. Therefore, each Converter comes with functions for checking if a string is a CURIE (converter.is_curie()) or a URI (converter.is_uri()) under its definition.

PythonJavaScriptRust

from curies_rs import get_obo_converter

converter = get_obo_converter()

assert converter.is_curie("GO:1234567")
assert not converter.is_curie("http://purl.obolibrary.org/obo/GO_1234567")
# This is a valid CURIE, but not under this converter's definition
assert not converter.is_curie("pdb:2gc4")

assert converter.is_uri("http://purl.obolibrary.org/obo/GO_1234567")
assert not converter.is_uri("GO:1234567")
# This is a valid URI, but not under this converter's definition
assert not converter.is_uri("http://proteopedia.org/wiki/index.php/2gc4")

import {getOboConverter} from "@biopragmatics/curies";

async function main() {
    const converter = await getOboConverter();

    console.log(converter.isCurie("GO:1234567"))

    console.log(converter.isUri("http://purl.obolibrary.org/obo/GO_1234567"))
}
main();

use curies::sources::get_obo_converter;

#[tokio::main]
async fn main() -> Result<(), Box<dyn std::error::Error>> {
    let converter = get_obo_converter().await?;

    assert_eq!(converter.is_curie("GO:1234567"), true);

    assert_eq!(converter.is_uri("http://purl.obolibrary.org/obo/GO_1234567"), true);
    Ok(())
}

🗜️ Standardized Expansion and Compression

The converter.expand_or_standardize() function extends the CURIE expansion function to handle the situation where you might get passed a CURIE or a URI. If it’s a CURIE, expansions happen with the normal rules. If it’s a URI, it tries to standardize it.

PythonJavaScriptRust

from curies_rs import Converter

converter = Converter.from_extended_prefix_map("""[{
    "prefix": "CHEBI",
    "prefix_synonyms": ["chebi"],
    "uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
    "uri_prefix_synonyms": ["https://identifiers.org/chebi:"]
}]""")

# Expand CURIEs
assert converter.expand_or_standardize("CHEBI:138488") == 'http://purl.obolibrary.org/obo/CHEBI_138488'
assert converter.expand_or_standardize("chebi:138488") == 'http://purl.obolibrary.org/obo/CHEBI_138488'

# standardize URIs
assert converter.expand_or_standardize("http://purl.obolibrary.org/obo/CHEBI_138488") == 'http://purl.obolibrary.org/obo/CHEBI_138488'
assert converter.expand_or_standardize("https://identifiers.org/chebi:138488") == 'http://purl.obolibrary.org/obo/CHEBI_138488'

# Handle cases that aren't valid w.r.t. the converter
try:
    converter.expand_or_standardize("missing:0000000")
    converter.expand_or_standardize("https://example.com/missing:0000000")
except Exception as e:
    print(e)

import {Converter} from "@biopragmatics/curies";

async function main() {
    const converter = await Converter.fromExtendedPrefixMap(`[{
        "prefix": "CHEBI",
        "prefix_synonyms": ["chebi"],
        "uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
        "uri_prefix_synonyms": ["https://identifiers.org/chebi:"]
    }]`)

    console.log(converter.expandOrStandardize("chebi:138488"))
    console.log(converter.expandOrStandardize("https://identifiers.org/chebi:138488"))
    try {
        console.log(converter.expandOrStandardize("http://purl.obolibrary.org/UNKNOWN_12345"))
    } catch (e) {
        console.log("Failed successfully)
    }
}
main();

use curies::Converter;

#[tokio::main]
async fn main() -> Result<(), Box<dyn std::error::Error>> {
    let converter = Converter::from_extended_prefix_map(r#"[{
        "prefix": "CHEBI",
        "prefix_synonyms": ["chebi"],
        "uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
        "uri_prefix_synonyms": ["https://identifiers.org/chebi:"]
    }]"#).await?;

    assert_eq!(converter.expand_or_standardize("http://amigo.geneontology.org/amigo/term/GO:0032571").unwrap(), "http://purl.obolibrary.org/obo/GO_0032571".to_string());
    assert_eq!(converter.expand_or_standardize("gomf:0032571").unwrap(), "http://purl.obolibrary.org/obo/GO_0032571".to_string());
    assert!(converter.expand_or_standardize("http://purl.obolibrary.org/UNKNOWN_12345").is_err());
    Ok(())
}

A similar workflow is implemented in converter.compress_or_standardize() for compressing URIs where a CURIE might get passed.

PythonJavaScriptRust

from curies_rs import Converter

converter = Converter.from_extended_prefix_map("""[{
    "prefix": "CHEBI",
    "prefix_synonyms": ["chebi"],
    "uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
    "uri_prefix_synonyms": ["https://identifiers.org/chebi:"]
}]""")

# Compress URIs
assert converter.compress_or_standardize("http://purl.obolibrary.org/obo/CHEBI_138488") == 'CHEBI:138488'
assert converter.compress_or_standardize("https://identifiers.org/chebi:138488") == 'CHEBI:138488'

# standardize CURIEs
assert converter.compress_or_standardize("CHEBI:138488") == 'CHEBI:138488'
assert converter.compress_or_standardize("chebi:138488") == 'CHEBI:138488'

# Handle cases that aren't valid w.r.t. the converter
try:
    converter.compress_or_standardize("missing:0000000")
    converter.compress_or_standardize("https://example.com/missing:0000000")
except Exception as e:
    print(e)
    print(type(e))

import {Converter} from "@biopragmatics/curies";

async function main() {
    const converter = await Converter.fromExtendedPrefixMap(`[{
        "prefix": "CHEBI",
        "prefix_synonyms": ["chebi"],
        "uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
        "uri_prefix_synonyms": ["https://identifiers.org/chebi:"]
    }]`)

    console.log(converter.compressOrStandardize("https://identifiers.org/chebi:138488"))
    console.log(converter.compressOrStandardize("gomf:0032571"))
    try {
        console.log(converter.compressOrStandardize("http://purl.obolibrary.org/UNKNOWN_12345"))
    } catch (e) {
        console.log("Failed successfully)
    }
}
main();

use curies::Converter;

#[tokio::main]
async fn main() -> Result<(), Box<dyn std::error::Error>> {
    let converter = Converter::from_extended_prefix_map(r#"[{
        "prefix": "CHEBI",
        "prefix_synonyms": ["chebi"],
        "uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
        "uri_prefix_synonyms": ["https://identifiers.org/chebi:"]
    }]"#).await?;

    assert_eq!(converter.compress_or_standardize("http://amigo.geneontology.org/amigo/term/GO:0032571").unwrap(), "go:0032571".to_string());
    assert_eq!(converter.compress_or_standardize("gomf:0032571").unwrap(), "go:0032571".to_string());
    assert!(converter.compress_or_standardize("http://purl.obolibrary.org/UNKNOWN_12345").is_err());
    Ok(())
}

🚚 Bulk operations

You can use the expand_list() and compress_list() functions to processes many URIs or CURIEs at once..

For example to create a new URI column in a pandas dataframe from a CURIE column:

import pandas as pd
from curies_rs import get_bioregistry_converter

converter = get_bioregistry_converter()
df = pd.DataFrame({'CURIE': ['doid:1234', 'doid:5678', 'doid:91011']})

# Expand the list of CURIEs to URIs
df['URI'] = converter.expand_list(df['CURIE'])
print(df)

🧩 Integrating with `rdflib`

RDFlib is a pure Python package for manipulating RDF data. The following example shows how to bind the extended prefix map from a Converter to a graph (rdflib.Graph).

import curies_rs, rdflib, rdflib.namespace, json

converter = curies_rs.get_obo_converter()
g = rdflib.Graph()

for prefix, uri_prefix in json.loads(converter.write_prefix_map()).items():
    g.bind(prefix, rdflib.Namespace(uri_prefix))

A more flexible approach is to instantiate a namespace manager (rdflib.namespace.NamespaceManager) and bind directly to that.

import curies_rs, rdflib, json

converter = curies_rs.get_obo_converter()
namespace_manager = rdflib.namespace.NamespaceManager(rdflib.Graph())

for prefix, uri_prefix in json.loads(converter.write_prefix_map()).items():
    namespace_manager.bind(prefix, rdflib.Namespace(uri_prefix))

URI references for use in RDFLib’s graph class can be constructed from CURIEs using a combination of converter.expand() and rdflib.URIRef.

import curies_rs, rdflib

converter = curies_rs.get_obo_converter()

uri_ref = rdflib.URIRef(converter.expand("CHEBI:138488"))

🧰 Tools for Developers and Semantic Engineers

🪄 Working with strings that might be a URI or a CURIE

☑️ CURIE and URI Checks

🗜️ Standardized Expansion and Compression

🚚 Bulk operations

🧩 Integrating with rdflib

🧩 Integrating with `rdflib`